The invention provides isolated and recombinant polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. The polypeptides of the invention, and the polynucleotides encoding the polypeptides of the invention, encompass many classes of enzymes, structural proteins and binding proteins. In one aspect, the enzymes and proteins of the invention include, e.g. aldolases, alpha-galactosidases, amidases, e.g. secondary amidases, amylases, catalases, carotenoid pathway enzymes, dehalogenases, endoglucanases, epoxide hydrolases, esterases, hydrolases, glucosidases, glycosidases, inteins, isomerases, laccases, lipases, monooxygenases, nitroreductases, nitrilases, P450 enzymes, pectate lyases, phosphatases, phospholipases, phytases, polymerases and xylanases. The invention also provides isolated and recombinant polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides encoding these polypeptides, having the activities described in Table 1, Table 2 or Table 3, below. The enzymes and proteins of the invention have utility in a variety of applications.